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I am looking at experimentally observed configurations of viral capsid proteins like that of the tobacco mosaic virus. https://www.rcsb.org/structure/6R7M

When taking the atom centers of a monomer and applying the transformations specified in the .pdb file, I get a structure where the VDW radii of different proteins overlap. I have tested a variety of sets of radii and it happens for all of them. I tested with Bondis radii, ProtOr radii and several radii taken from popular force fields (AMBER, PARSE, CHARMM).

I am wondering:

  • What is the least wrong set of radii to choose here and why?
  • Is there a popular way to resolve this?
  • The Clashscore depends on overlaps within a protein right? What radii are chosen for this measure?

Thank you in advance

Ivan

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    $\begingroup$ can you give us the chain ID, residue number, and atomID for the atoms in the .pdb file that are overlapping in the linked TMV structure? Is this something you've noticed in other structures as well, or just this one? $\endgroup$
    – timeskull
    Commented Mar 22 at 14:34
  • $\begingroup$ In the example behind the link, the chain ID is 'A' and considering two adjacent monomers transformed by the specified BIOMTs we get an overlap between Atom IDs 164 and 72 by 0.3 Angström for example, when choosing Bondis VDW radii for the atoms. There are around 20 of these overlaps in total. So far every assembled TMV structure I checked has these overlaps. $\endgroup$ Commented Mar 26 at 10:19

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Looking at the validation report for model 6R7M, we see that there are no symmetry-related clashes listed. (Although there are two clashes within the asymmetric unit, HA of ASP20 - HD3 of PRO21 and HG13 of ILE95 - HB2 of ALA111) The relevant portion of the PDB's validation explanation page is here:

All-atom contacts within the ASU are calculated by the Reduce and Probe programs within MolProbity (Word et al., 1999; Chen et al., 2010). This method was developed to quantify the detailed non-covalent fit of atomic interactions within or between molecules (H-bonds, favorable van der Waals, and steric clashes). Since most such interactions involve H atoms on one or both sides, all hydrogens must be present or added (Reduce optimizes rotation of OH, SH, NH3, etc. within H-bond networks, but methyls stay staggered). At present, in order to ensure comparable scores between NMR and X-ray, hydrogen atoms are removed from the analysed structure, and replaced by a different set placed by Reduce in idealised and optimized nuclear-H positions. All-atom unfavorable overlaps ≥0.4Å are then identified as clashes, using van der Waals radii tuned for the nuclear H positions suitable for NMR (rather than the electron-cloud H positions suitable for X-ray).).

(bolding mine)

The main takeaway is that MolProbity does not consider that amount of overlap to be a problem. So to your second bullet point, I don't think anything needs to be resolved. As for which radii should be used, I don't have good advice. It looks like that is still being debated. However, looking up the original paper for the MolProbity tools used by the PDB for validation, the radii for O and non-carbonyl C are 1.4 and 1.75 Angströms, respectively. That sums to 3.15, I measure 2.92 between the atomic centers, so slightly less overlap than you got. My initial assumption was that these would be poorly-resolved residues near the edge of the macromolecule and that the VDW overlap would be due to fitting errors, but it looks pretty good to me: The atomic model of PDB6R7M is shown fitted into the density map EMD4628

As noted in comments, some nonbonded atoms in model 6R7M have more than 0.4 Angströms overlap, but are not tagged as clashing, e.g. the sidechain oxygens of THR29 and TYR73. This is because these overlaps are not unfavorable; that is, molprobity predicts hydrogen bonding between them. I couldn't find any specifics about how molprobity determines if a particular overlap is unfavorable. The best description I found is in the documentation of the chimera tool findclash:

The Clash/Contact Parameters control what will be considered a clash or contact. The overlap between two atoms is defined as the sum of their VDW radii minus the distance between them and minus an allowance for potentially hydrogen-bonded pairs:

overlapij = rVDWi + rVDWj – dij – allowanceij

Find atoms with VDW overlap >=[ cutoff ] angstroms - pairs of atoms with overlap ≥ cutoff will be identified. A larger positive cutoff restricts the results to more severe clashes, whereas a negative cutoff can also identify favorable contacts.

Subtract [ allowance ] from overlap for potentially H-bonding pairs - an allowance > 0 reflects the observation that atoms sharing a hydrogen bond can come closer to each other than would be expected from their VDW radii. The allowance is only subtracted for pairs comprised of a donor (or donor-borne hydrogen) and an acceptor. This is equivalent to using smaller radii to characterize hydrogen-bonding interactions (for example, see Li and Nussinov, Proteins 32:111 (1998)). As in FindHBond, possible donor groups are hydrogen-bearing nitrogen, oxygen, and sulfur atoms, and possible acceptor groups are nitrogen, oxygen, and sulfur atoms with a lone pair.

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  • $\begingroup$ Thank you for the detailed response. Follow up question: Between Atoms 217 and 590 I am calculating a distance of roughly 2.3A. Both are oxygen atoms so no matter the set of radii that would be a symmetric clash no? $\endgroup$ Commented Apr 11 at 10:12
  • $\begingroup$ the bolded text in the 1st quote of my answer says 'unfavorable overlaps'; if a bond is expected, some overlap is expected, so it doesn't register as a clash. I don't know the specifics for molprobity, I'll add it to the answer later. $\endgroup$
    – timeskull
    Commented Apr 11 at 13:47
  • $\begingroup$ This is really interesting. I did not know, that bonds between different proteins form at all during self assembly. $\endgroup$ Commented Apr 12 at 8:23
  • $\begingroup$ to be clear, these are hydrogen bonds, not covalent bonds. Bacteriophage HK97 does form isopeptide covalent bonds in the final stages of its self-assembly, but that is unusual. $\endgroup$
    – timeskull
    Commented Apr 12 at 15:42
  • $\begingroup$ Thank you for clearing that up. Is there a way to identify the hydrogen bonded Atoms from a PDB? And also if it is easy to explain: how do hydrogen bonds lead to oxygen atoms being closer together? $\endgroup$ Commented Apr 15 at 11:12

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